X-ray crystallography

About 85% of the models (entries) in the World Wide Protein Data Bank were determined by X-ray crystallography. (Most of the remaining 15% were determined by solution nuclear magnetic resonance.) Analysis of x-ray diffraction patterns from protein crystals produces an electron density map, into which an atomic model of the protein is fitted. Major errors sometimes occur when fitting models in to low-resolution electron density maps (see Quality assessment for molecular models). The value of Free R is the best clue as to whether major errors may be present in a published model.

Obtaining diffraction-quality crystals of proteins remains very difficult, despite many recent advances. For every new protein sequence targeted for X-ray crystallography, about one in twenty is solved.

Publication of solved structures involves depositing an atomic coordinate file (PDB file) in the World Wide Protein Data Bank.